Methylobacterium marchantiae sp. nov., a pink-pigmented, facultatively methylotrophic bacterium isolated from the thallus of a liverwort

2011 ◽  
Vol 61 (4) ◽  
pp. 870-876 ◽  
Author(s):  
S. Schauer ◽  
P. Kämpfer ◽  
S. Wellner ◽  
C. Spröer ◽  
U. Kutschera
Keyword(s):  
Gene Sequence ◽  
Novel Species ◽  
Marchantia Polymorpha ◽  
Methylotrophic Bacterium ◽  
Rrna Gene ◽  
Closely Related Species ◽  
Gene Sequence Analysis ◽  
Type Strains ◽  
Physiological And Biochemical ◽  
Sequence Similarities

A pink-pigmented, facultatively methylotrophic bacterium, designated strain JT1T, was isolated from a thallus of the liverwort Marchantia polymorpha L. and was analysed by using a polyphasic approach. Comparative 16S rRNA gene sequence analysis placed the strain in a clade with Methylobacterium adhaesivum AR27T, Methylobacterium fujisawaense DSM 5686T, Methylobacterium radiotolerans JCM 2831T and Methylobacterium jeotgali S2R03-9T, with which it showed sequence similarities of 97.8, 97.7, 97.2 and 97.4 %, respectively. However, levels of DNA–DNA relatedness between strain JT1T and these and the type strains of other closely related species were lower than 70 %. Cells of JT1T stained Gram-negative and were motile, rod-shaped and characterized by numerous fimbriae-like appendages on the outer surface of their wall (density up to 200 µm−2). Major fatty acids were C18 : 1ω7c and C16 : 0. Based on the morphological, physiological and biochemical data presented, strain JT1T is considered to represent a novel species of the genus Methylobacterium, for which the name Methylobacterium marchantiae sp. nov. is proposed. The type strain is JT1T ( = DSM 21328T  = CCUG 56108T).

scholarly journals Pseudomonas pohangensis sp. nov., isolated from seashore sand in Korea

2006 ◽  
Vol 56 (9) ◽  
pp. 2153-2156 ◽  
Author(s):  
Hang-Yeon Weon ◽  
Byung-Yong Kim ◽  
Seung-Hee Yoo ◽  
Youn-Kyung Baek ◽  
Seon-Young Lee ◽  
...  
Keyword(s):  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Novel Bacterium ◽  
Gene Sequence Analysis ◽  
Seashore Sand ◽  
Type Strains ◽  
Sequence Similarities

A novel bacterium, designated strain H3-R18T, was isolated from seashore sand collected from Homi cape, Pohang city, Korea. Cells were Gram-negative, aerobic, non-motile, cream-coloured, mesophilic and slightly halotolerant. 16S rRNA gene sequence analysis indicated that the organism was a member of the genus Pseudomonas, but the sequence showed ⩽96.3 % sequence similarity to that of the type strains of all recognized Pseudomonas species. Highest sequence similarities were to Pseudomonas brenneri CFML 97-391T (96.3 %) and Pseudomonas migulae CIP 105470T (96.3 %). The major fatty acids were summed feature 3 and C16 : 0, with lesser amounts of C12 : 0, C12 : 0 3-OH, C18 : 1ω7c and C14 : 0. The major isoprenoid quinone was Q-9. The DNA G+C content was 64.0 mol%. The phylogenetic, phenotypic and genetic properties of strain H3-R18T suggest that it represents a novel species, for which the name Pseudomonas pohangensis sp. nov. is proposed. The type strain is H3-R18T (=KACC 11517T=DSM 17875T).

Pseudomonas peli sp. nov. and Pseudomonas borbori sp. nov., isolated from a nitrifying inoculum

2006 ◽  
Vol 56 (8) ◽  
pp. 1875-1881 ◽  
Author(s):  
Bram Vanparys ◽  
Kim Heylen ◽  
Liesbeth Lebbe ◽  
Paul De Vos
Keyword(s):  
Gene Sequence ◽  
Novel Species ◽  
Rrna Gene ◽  
Biochemical Tests ◽  
Banding Patterns ◽  
Gene Sequence Analysis ◽  
Species Analysis ◽  
Sds Page ◽  
Type Strains ◽  
Physiological And Biochemical

Sixteen Gram-negative, rod-shaped, non-spore-forming isolates were obtained from a nitrifying inoculum. Analysis of repetitive sequence-based PCR and SDS-PAGE banding patterns, 16S rRNA gene sequence analysis and DNA–DNA hybridizations showed that the isolates belonged to various groups within the genus Pseudomonas. One group of isolates could be assigned to Pseudomonas migulae and a second to Pseudomonas veronii. Two groups could be differentiated genotypically from each other and from all other currently known Pseudomonas species. Analysis of the fatty acid composition and physiological and biochemical tests allowed differentiation of these groups from their closest phylogenetic neighbours and they therefore represent two novel species within the genus Pseudomonas, for which the names Pseudomonas peli sp. nov. and Pseudomonas borbori sp. nov. are proposed, with strains LMG 23201T (=DSM 17833T=R-20805T) and LMG 23199T (=DSM 17834T=R-20821T), respectively, as the type strains.

scholarly journals Devosia soli sp. nov., isolated from greenhouse soil in Korea

2006 ◽  
Vol 56 (11) ◽  
pp. 2689-2692 ◽  
Author(s):  
Seung-Hee Yoo ◽  
Hang-Yeon Weon ◽  
Byung-Yong Kim ◽  
Seung-Beom Hong ◽  
Soon-Wo Kwon ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Biochemical Tests ◽  
Greenhouse Soil ◽  
Gene Sequence Analysis ◽  
Physiological And Biochemical ◽  
Sequence Similarities

A Gram-negative, obligately aerobic, rod-shaped bacterium was isolated from greenhouse soil used to cultivate lettuce. The strain, GH2-10T, was characterized on the basis of phenotypic and genotypic data. 16S rRNA gene sequence analysis revealed that the isolate belonged to the genus Devosia, with highest sequence similarity (98.5 %) to Devosia riboflavina IFO 13584T. Sequence similarities with other strains tested were below 97.0 %. Strain GH2-10T had Q-10 as the predominant ubiquinone and C18 : 1 ω7c and C16 : 0 as the major fatty acids. The G+C content of the genomic DNA was 59.5 mol%. The results of DNA–DNA hybridization experiments (47 % relatedness between D. riboflavina DSM 7230T and strain GH2-10T) and physiological and biochemical tests suggested that strain GH2-10T represents a novel species of the genus Devosia, for which the name Devosia soli sp. nov. is proposed. The type strain is GH2-10T (=KACC 11509T=DSM 17780T).

scholarly journals Bacteroides coprophilus sp. nov., isolated from human faeces

2007 ◽  
Vol 57 (6) ◽  
pp. 1323-1326 ◽  
Author(s):  
Hidenori Hayashi ◽  
Kensaku Shibata ◽  
Mohammad Abdul Bakir ◽  
Mitsuo Sakamoto ◽  
Shinichi Tomita ◽  
...  
Keyword(s):  
Type Strain ◽  
Gene Sequence ◽  
Novel Species ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Phenotypic Characteristics ◽  
Human Faeces ◽  
Gene Sequence Analysis ◽  
Type Strains ◽  
Sequence Similarities

Three Gram-negative, anaerobic, rod-shaped bacteria (strains CB40, CB41 and CB42T) were isolated from human faeces. Based on phylogenetic analysis and specific phenotypic characteristics, these strains were included in the genus Bacteroides, and 16S rRNA gene sequence analysis indicated that these strains represented a novel species. The strains were most closely related to the type strains of Bacteroides barnesiae and Bacteroides salanitronis, with sequence similarities of 93.4 and 89.8 %, respectively. The G+C content of strain CB42T is 44.7 mol%. Major fatty acids were anteiso-C15 : 0, C16 : 0, iso-C17 : 0 3-OH and C18 : 1 ω9c. On the basis of the data presented, a novel Bacteroides species, Bacteroides coprophilus sp. nov., is proposed, with CB42T (=JCM 13818T=DSM 18228T) as the type strain.

scholarly journals Pantoea theicola sp. nov., isolated from black tea

2015 ◽  
Vol 65 (Pt_10) ◽  
pp. 3313-3319 ◽  
Author(s):  
Yuko Kato Tanaka ◽  
Nobuhiro Horie ◽  
Kaoru Mochida ◽  
Yoshihiro Yoshida ◽  
Eri Okugawa ◽  
...  
Keyword(s):  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Black Tea ◽  
Rrna Gene ◽  
Biochemical Tests ◽  
Phenotypic Differentiation ◽  
Type Strains ◽  
Physiological And Biochemical ◽  
Sequence Similarities

A Gram-negative, facultatively anaerobic strain was isolated from black tea. On the basis of 16S rRNA gene sequence similarity comparisons, strain QC88-366T was grouped into the genus Pantoea, being related most closely to the type strains of Pantoea gaviniae (98.5 %) and Pantoea calida (98.3 %); sequence similarities were ≤ 97.0 % to the type strains of other species of the genus Pantoea. Multilocus sequence analysis based on partial sequences of the gyrB, rpoB, infB and atpD genes also revealed P. gaviniae and P. calida as the closest phylogenetic relatives. The fatty acid profile showed the major fatty acids of strain QC88-366T were C16 : 0, C16 : 1 and C18 : 1, the same as those of its closest related species. However, the ratio of C16 : 1, C17 : 0 cyclo, C18 : 1 and C18 : 2 differed slightly compared with those of the related neighbours. In addition, the results of physiological and biochemical tests also allowed the phenotypic differentiation of strain QC88-366T from its closest phylogenetic neighbours. The G+C content of the DNA was 57.2 mol%. Strain QC88-366T therefore represents a novel species of the genus Pantoea, for which the name Pantoea theicola sp. nov. is proposed. The type strain is QC88-366T ( = DSM 29212T = NBRC 110557T).

scholarly journals Sphingomonas zeae sp. nov., isolated from the stem of Zea mays

2015 ◽  
Vol 65 (Pt_8) ◽  
pp. 2542-2548 ◽  
Author(s):  
Peter Kämpfer ◽  
Hans-Jürgen Busse ◽  
John A. McInroy ◽  
Stefanie P. Glaeser
Keyword(s):  
Zea Mays ◽  
Gene Sequence ◽  
Bacterial Isolate ◽  
Novel Species ◽  
Rrna Gene ◽  
Physiological Characterization ◽  
Gene Sequence Analysis ◽  
16S Rna ◽  
Type Strains ◽  
Sequence Similarities

A yellow-pigmented bacterial isolate (strain JM-791T) obtained from the healthy internal stem tissue of 1-month-old corn (Zea mays, cultivar ‘Sweet Belle’) grown at the Plant Breeding Unit of the E.V. Smith Research Center in Tallassee (Elmore county), Alabama, USA, was taxonomically characterized. The study employing a polyphasic approach, including 16S RNA gene sequence analysis, physiological characterization, estimation of the ubiquinone and polar lipid patterns, and fatty acid composition, revealed that strain JM-791T shared 16S rRNA gene sequence similarities with type strains of Sphingomonas paucimobilis (98.3 %), Sphingomonas pseudosanguinis (97.5 %) and Sphingomonas yabuuchiae (97.4 %), but also showed pronounced differences, both genotypically and phenotypically. On the basis of these results, a novel species of the genus Sphingomonas is described, for which we propose the name Sphingomonas zeae sp. nov. with the type strain JM-791T ( = LMG 28739T = CCM 8596T).

scholarly journals Stenotrophomonas daejeonensis sp. nov., isolated from sewage

2011 ◽  
Vol 61 (3) ◽  
pp. 598-604 ◽  
Author(s):  
Myungjin Lee ◽  
Sung-Geun Woo ◽  
Myoungsoo Chae ◽  
Min-Cheol Shin ◽  
Hae-Min Jung ◽  
...  
Keyword(s):  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Closely Related Species ◽  
Predominant Component ◽  
Gene Sequence Analysis ◽  
The Family ◽  
Stenotrophomonas Nitritireducens ◽  
Type Strains

A Gram-stain-negative, motile, aerobic bacterial strain, designated MJ03T, was isolated from sewage and was characterized taxonomically by using a polyphasic approach. Comparative 16S rRNA gene sequence analysis showed that strain MJ03T belongs to the family Xanthomonadaceae, class Gammaproteobacteria, and was related most closely to Stenotrophomonas acidaminiphila AMX 19T (97.9 % sequence similarity), Stenotrophomonas humi R-32729T (97.1 %), Stenotrophomonas nitritireducens L2T (96.9 %), Stenotrophomonas maltophila ATCC 13637T (96.8 %) and Stenotrophomonas terrae R-32768T (96.7 %). The G+C content of the genomic DNA of strain MJ03T was 64.7 mol%. The detection of a quinone system with ubiquinone Q-8 as the predominant component and a fatty acid profile with iso-C15 : 0, iso-C11 : 0, iso-C14 : 0, iso-C17 : 1 ω9c, iso-C11 : 0 3-OH and iso-C13 : 0 3-OH as major components supported the affiliation of strain MJ03T to the genus Stenotrophomonas. However, levels of DNA–DNA relatedness between strain MJ03T and the type strains of five closely related species of the genus Stenotrophomonas ranged from 11 to 34 %, showing clearly that the isolate represents a novel genospecies. Strain MJ03T could be differentiated clearly from its phylogenetic neighbours on the basis of several phenotypic, genotypic and chemotaxonomic features. Therefore, strain MJ03T is considered to represent a novel species of the genus Stenotrophomonas, for which the name Stenotrophomonas daejeonensis sp. nov. is proposed. The type strain is MJ03T (=KCTC 22451T =JCM 16244T).

scholarly journals Novosphingobium gossypii sp. nov., isolated from Gossypium hirsutum

2015 ◽  
Vol 65 (Pt_9) ◽  
pp. 2831-2837 ◽  
Author(s):  
Peter Kämpfer ◽  
Karin Martin ◽  
John A. McInroy ◽  
Stefanie P. Glaeser
Keyword(s):  
Gossypium Hirsutum ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
High Sequence Similarity ◽  
Polar Lipid Profile ◽  
Gene Sequence Analysis ◽  
Bacterium Strain ◽  
Type Strains ◽  
Sequence Similarities

A Gram-stain-negative, rod-shaped, non-spore-forming bacterium (strain JM-1396T) producing a yellow pigment, was isolated from the healthy internal stem tissue of post-harvest cotton (Gossypium hirsutum, cultivar ‘DES-119’) grown at the Plant Breeding Unit at the E. V. Smith Research Center in Tallassee (Macon county), AL, USA. 16S rRNA gene sequence analysis of strain JM-1396T showed high sequence similarity values to the type strains of Novosphingobium mathurense, Novosphingobium panipatense (both 98.6 %) and Novosphingobium barchaimii (98.5 %); sequence similarities to all other type strains of species of the genus Novosphingobium were below 98.3 %. DNA–DNA pairing experiments of the DNA of strain JM-1396T and N. mathurense SM117T, N. panipatense SM16T and N. barchaimii DSM 25411T showed low relatedness values of 8 % (reciprocal 7 %), 24 % (reciprocal 26 %) and 19 % (reciprocal 25 %), respectively. Ubiquinone Q-10 was detected as the dominant quinone; the fatty acids C18 : 1ω7c (71.0 %) and the typical 2-hydroxy fatty acid, C14 : 0 2-OH (11.7 %), were detected as typical components. The polar lipid profile contained the diagnostic lipids diphosphatidylglycerol, phosphatidylethanolamine, sphingoglycolipid and phosphatidylcholine. The polyamine pattern contained the major compound spermidine and only minor amounts of other polyamines. All these data revealed that strain JM-1396T represents a novel species of the genus Novosphingobium. For this reason we propose the name Novosphingobium gossypii sp. nov. with the type strain JM-1396T ( = LMG 28605T = CCM 8569T = CIP 110884T).

Paracoccus caeni sp. nov., isolated from sludge

2011 ◽  
Vol 61 (8) ◽  
pp. 1968-1972 ◽  
Author(s):  
Myungjin Lee ◽  
Song-Geun Woo ◽  
Giho Park ◽  
Myung Kyum Kim
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Gene Sequence Analysis ◽  
The Family ◽  
Type Strains ◽  
Sequence Similarities

A Gram-negative, non-motile bacterium, designated MJ17T, was isolated from sludge at the Daejeon sewage disposal plant in South Korea. Comparative 16S rRNA gene sequence analysis showed that strain MJ17T belonged to the genus Paracoccus in the family Rhodobacteraceae of the class Alphaproteobacteria. 16S rRNA gene sequence similarities between strain MJ17T and type strains of species of the genus Paracoccus were 94.1–97.4 %. The highest similarities were between strain MJ17T and Paracoccus homiensis DD-R11T, Paracoccus zeaxanthinifaciens ATCC 21588T and Paracoccus alcaliphilus JCM 7364T (97.4, 97.2 and 96.3 %, respectively). Strain MJ17T exhibited <22 % DNA–DNA relatedness with P. homiensis KACC 11518T and P. zeaxanthinifaciens JCM 21774T. The G+C content of the genomic DNA was 58.7 mol%. Strain MJ17T contained ubiquinone Q-10. The major fatty acids were C18 : 0 (11.3 %), C16 : 0 (10.2 %) and summed feature 7 (containing one or more of C18 : 1ω7c, C18 : 1ω9c and C18 : 1ω12t; 54.3 %). Poly-β-hydroxybutyrate granules are formed. On the basis of phenotypic and genotypic properties and phylogenetic distinctiveness, strain MJ17T should be classified in a novel species of the genus Paracoccus, for which the name Paracoccus caeni sp. nov. is proposed. The type strain is MJ17T ( = KCTC 22480T  = JCM 16385T  = KEMB 9004-001T).

scholarly journals Marinomonas ostreistagni sp. nov., isolated from a pearl-oyster culture pond in Sanya, Hainan Province, China

2006 ◽  
Vol 56 (10) ◽  
pp. 2271-2275 ◽  
Author(s):  
Ken W. K. Lau ◽  
Jianping Ren ◽  
Natalie L. M. Wai ◽  
Simon C. L. Lau ◽  
Pei-Yuan Qian ◽  
...  
Keyword(s):  
Marine Bacterium ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Pearl Oyster ◽  
Rrna Gene ◽  
Hainan Province ◽  
Oyster Culture ◽  
Gene Sequence Analysis ◽  
Type Strains

A Gram-negative, aerobic, halophilic, neutrophilic, rod-shaped, non-pigmented, polar-flagellated bacterium, UST010306-043T, was isolated from a pearl-oyster culture pond in Sanya, Hainan Province, China in January 2001. This marine bacterium had an optimum temperature for growth of between 33 and 37 °C. On the basis of 16S rRNA gene sequence analysis, the strain was closely related to Marinomonas aquimarina and Marinomonas communis, with 97.5–97.7 and 97.1 % sequence similarity, respectively. Levels of DNA–DNA relatedness to the type strains of these species were well below 70 %. Analyses of phylogenetic, phenotypic and chemotaxomonic characteristics showed that strain UST010306-043T was distinct from currently established Marinomonas species. A novel species with the name Marinomonas ostreistagni sp. nov. is proposed to accommodate this bacterium, with strain UST010306-043T (=JCM 13672T=NRRL B-41433T) as the type strain.

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